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Geophysical methods are useful tools for mapping the boundary between fresh and saline water. A geophysical survey was conducted in order to study the mechanisms of saltwater contamination in a strongly karstic coastal area. The region of interest is located in Western Crete about 3 Κm from the seashore. Seismic and electrical resistivity methods, along with detailed geological mapping have been employed to study the complex geological structure of the area under investigation. Electrical tomography detected a low resistivity zone which is attributed to a saline water layer. From the combination of the geophysical and geological data, a depicted major normal NE-SW fault zone mainly causes the groundwater salinization.